Impact of genomic preselection on subsequent genetic evaluations with ssGBLUP using real data from pigs

Table 1 Data used in subsequent ssGBLUP^a evaluations following each preselection scenario, after quality control

Data in the subsequent ssGBLUP evaluation/preselection scenario	With records on animals in the validation generation			Without records on animals in the validation generation
	Reference^b	VGP^c	MGP^d	Reference^b	VGP^c	MGP^d
Sire line (number of validation animals per trait is ± 1383)
Number of animals in the pedigree	81,875	60,950	12,777	81,875	60,950	12,777
Number of animals with record for at least one trait^e	75,129	54,217	6065	52,846	52,846	4694
Number of animals with genotypes	33,506	23,315	5131	33,506	23,315	5131
Number of SNP genotyped	20,550	20,963	20,926	20,550	20,963	20,926
Dam line (number of validation animals per trait is ± 2051)
Number of animals in the pedigree	160,426	124,031	33,485	160,426	124,031	33,485
Number of animals with record for at least one trait	139,403	103,018	12,514	100,710	100,710	10,206
Number of animals with genotypes	50,895	36,369	9072	50,895	36,369	9072
Number of SNP genotyped	19,199	19,256	20,647	19,199	19,256	20,647

^aSingle-step genomic best linear unbiased prediction
^bIn the reference scenario, the subsequent ssGBLUP evaluation used the entire available data until the validation generation
^cValidation generation preselection (VGP) scenario, in which all animals in the validation generation without progeny in the data were discarded
^dMulti-generation preselection (MGP) scenario, in which all animals in the validation and training generations without progeny in the data were discarded
^eAbout 87% and 70% of the animals in the sire and dam lines, respectively, had records for the four traits used in this study, and even larger numbers had records for any two and three traits. We decided to keep any animal with a record for at least one of the traits (92% and 87% of the animals in the sire and dam lines, respectively) because every animal in the analyses would benefit from records on relatives and records of correlated traits (see Additional file 1: Table S1), in addition to its own record on the primary trait

ISSN: 1297-9686